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- PDB-7e8m: Crystal structure of SARS-CoV-2 antibody P2C-1F11 with mutated RBD -

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Basic information

Entry
Database: PDB / ID: 7e8m
TitleCrystal structure of SARS-CoV-2 antibody P2C-1F11 with mutated RBD
Components
  • Spike protein S1
  • antibody P2C-1F11 heavy chain
  • antibody P2C-1F11 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 spike / receptor binding domain / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsWang, X.Q. / Zhang, L.Q. / Ge, J.W. / Wang, R.K. / Lan, J.
CitationJournal: Immunity / Year: 2021
Title: Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species.
Authors: Wang, R. / Zhang, Q. / Ge, J. / Ren, W. / Zhang, R. / Lan, J. / Ju, B. / Su, B. / Yu, F. / Chen, P. / Liao, H. / Feng, Y. / Li, X. / Shi, X. / Zhang, Z. / Zhang, F. / Ding, Q. / Zhang, T. / Wang, X. / Zhang, L.
History
DepositionMar 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Spike protein S1
H: antibody P2C-1F11 heavy chain
L: antibody P2C-1F11 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2554
Polymers68,0343
Non-polymers2211
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-26 kcal/mol
Surface area27520 Å2
Unit cell
Length a, b, c (Å)195.844, 85.973, 57.872
Angle α, β, γ (deg.)90.000, 99.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Spike protein S1


Mass: 21907.557 Da / Num. of mol.: 1 / Mutation: K417N, E484K, N501Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2
#2: Antibody antibody P2C-1F11 heavy chain


Mass: 22851.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Antibody antibody P2C-1F11 light chain


Mass: 23274.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 12%w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.09→26.17 Å / Num. obs: 50710 / % possible obs: 90.92 % / Redundancy: 5.3 % / CC1/2: 0.997 / Net I/σ(I): 17.2
Reflection shellResolution: 2.09→2.17 Å / Num. unique obs: 3033 / CC1/2: 0.762

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CDI

7cdi


Resolution: 2.09→26.17 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 2513 4.96 %
Rwork0.1689 48172 -
obs0.1704 50685 90.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.55 Å2 / Biso mean: 41.7495 Å2 / Biso min: 20.87 Å2
Refinement stepCycle: final / Resolution: 2.09→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 14 499 5224
Biso mean--81.75 45.93 -
Num. residues----616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.130.2202690.19881490155951
2.13-2.180.2674930.20331774186761
2.18-2.230.26531240.2032062218670
2.23-2.280.23071090.20382233234277
2.28-2.330.24761310.19722522265386
2.33-2.40.24441600.19952819297996
2.4-2.470.2271250.196129213046100
2.47-2.550.2461390.184329443083100
2.55-2.640.23061580.195229543112100
2.64-2.740.23911640.184429323096100
2.74-2.870.21361450.186129213066100
2.87-3.020.20631610.180929213082100
3.02-3.210.19921360.182429743110100
3.21-3.460.17951470.164829463093100
3.46-3.80.18931830.160429183101100
3.8-4.350.17451670.145629183085100
4.35-5.470.15411440.132329633107100
5.48-26.170.20391580.17442960311898
Refinement TLS params.Method: refined / Origin x: -59.8228 Å / Origin y: 3.8823 Å / Origin z: 26.8046 Å
111213212223313233
T0.2658 Å20.0081 Å2-0.0276 Å2-0.2107 Å20.008 Å2--0.2082 Å2
L1.7423 °2-0.6063 °2-0.449 °2-0.5966 °20.1571 °2--0.402 °2
S-0.0325 Å °0.051 Å °0.0055 Å °0.0121 Å °0.0188 Å °-0.0164 Å °0.0499 Å °-0.0214 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allE333 - 601
2X-RAY DIFFRACTION1allH2 - 217
3X-RAY DIFFRACTION1allL1 - 214
4X-RAY DIFFRACTION1allS1 - 505

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